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如何使用jionmap构建遗传图谱  

2012-07-17 15:36:06|  分类: 数量遗传学 |  标签: |举报 |字号 订阅

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1. Download the evaluation version of JoinMap 4.1 from the Kyazma website http://www.kyazma.nl/index.php/mc.JoinMap/sc.Evaluate/
2. Open program
3. Create a New Project – name it anything you’d like
4. Load the F2 population sample data file provided (Under file tab or on toolbar)
Explore the tabs for the BBSDUBF2 dataset. When you click on a tab, if a calculation can be made, the calculator will appear. Click the calculator and see what happens. These data are from a real linkage mapping population for winter squash (Cucurbita moschata). The parents were ‘Butterbush’ (BB) and ‘Sucrine duBerry’ (SDUB). The mapping population is an F2 population, and the marker types were RAPD and SSR markers. There are both dominant and co-dominant markers in the dataset.
5. The final tab is labeled Groupings_(tree). Click on the tab and then click the calculate button.
6. A tree with various nodes will be calculated. The nodes are labeled as follows: 3.0/1(45) where 3.0=the LOD threshold the group was created at, 1=the sequential number assigned to the groups at the same LOD threshold, and (45)=the number of marker loci in the group at that threshold.
7. The evaluation version is limited to two linkage groups evaluated at one time. This means that although there are more chromosomes in squash, this dataset only represents two of the chromosomes (linkage groups). Therefore, we will only be mapping 2 linkage groups. You will see more than 2 nodes in the Groupings_(tree).
How would you decide which nodes to map? If you know the base chromosome number of an organism, you would know how many linkage groups to expect. What are the right ones to pick? What do you know about LOD score thresholds that might help you pick?
8. Highlight the nodes that you want to map by clicking on the node and pressing the space bar. The node will highlight red when it is selected.
9. Under the Population tab, click on the option Create Groups Using the Groupings Tree.
10. You should see Group 1 and Group 2 appear on the left side of the screen in another tree format. There are new tabs formed, and you can use the calculator button when available here too.
11. Open the Calculation Options under the Options tab on the toolbar.
12. Under Group tab check the Regression mapping button under Mapping algorithm.
13. Under Regression Mapping tab check the Kosambi’s function button under Mapping function.
14. Highlight Group 1 and click the calculate map button.
15. Scroll to the bottom of the Mapping 1 Session Log – you’ll see a message that says: Insufficient linkage to above group (minimum of two distinct links required) : 77.OPAK06B. This means that
marker number 77 was incorrectly grouped with the rest – two point linkage analysis estimated that it was linked, but multipoint linkage analysis cannot show linkage. Click on the Group 1 in the tree at the left, and click on the Loci tab that shows up. Find marker 77 OPAK06B and check the box to exclude that marker from the analysis.
16. Click the calculate map button again.
17. Now three maps should appear under the Group 1 node of the tree at the left.
18. Use the same process to create a map for Group 2.
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